On Thu, Aug 19, 2010 at 7:51 AM, Kevin Lam <aboulia@gmail.com> wrote:

Hi Nate,
While I do not have ideas to improve browser uploads but i do have some untested ideas for uploads for ppl who like me are unlikely to have access to the institute's ftp or http webserver to serve files.

It might be a tad convoluted but have you considered dropbox integration for galaxy?
I have terrible upload speeds for amazon S3 but that might be a consideration for some.

with regards to local install, is there a way I can point galaxy directly to the file? or make it access it directly instead of my workaround by using python /perl scripts to emulate a webserver?

Cheers
Kevin

On Thu, Aug 19, 2010 at 3:42 AM, Nate Coraor <nate@bx.psu.edu> wrote:

Hi Farhat and others,

Thanks for reporting your experiences. Does it seem to be everyone's experience that direct file uploads of files > 2GB fails? We are looking in to more reliable methods for handling direct uploads, so any suggestions are welcome.

--nate

Farhat Habib wrote:

I ran into this issue too repeatedly. Both with local install of Galaxy and the main instance. Files over roughly 2GB or so refused to upload, the page would still show them as uploading but nothing was happening. Compressing the same file so it was under 2GB and uploading worked fine both on the local instance and main.

-Farhat

--
Farhat Habib, PhD
IISER Fellow, Biology
Indian Institute of Science Education & Research,
Sai Trinity Building, Garware Circle,
Sutarwadi, Pashan, Pune-411 021.
http://www.iiserpune.ac.in/~farhat

Office: +91 20 2590 8015
Cell: +91 973 0996 233

On Wed, Aug 18, 2010 at 12:25 PM, Abhay Krishna <abhay.krishna@gmail.com <mailto:abhay.krishna@gmail.com>> wrote:

Dear Asifullah

As Kevin says, you are much better off by using http or ftp url,
Also i know there are issues if you refresh the browser while
uploading, So I guess if uploading does not work normally,

try putting on http or ftp server and give a url, and do not touch
the browser untill uploading is over

also you can alternatively use a perl or python script locally

http://seqanswers.com/forums/showthread.php?t=269

best
Abhay Krishna

On 18 August 2010 08:47, Kevin Lam <aboulia@gmail.com
<mailto:aboulia@gmail.com>> wrote:

I have created a local install of galaxy and i can tell you it
is not about network connection.
As I am using a local install but the 'upload' is horribly slow.
a 3Gb file can't finish in 24 hours.

in the end, I used a python script to 'serve' the file via http
protocol and entered a local LAN url for galaxy and it loaded up
in minutes.

For your case, I think I have no issues up to 250 Mb on their
galaxy main server, but as the wiki and manual (plus my
experience with a local instance) suggests you would do well to
put the file on a webserver and give the url instead of upload
via browser.

Cheers
Kevin

On Wed, Aug 18, 2010 at 2:17 PM, asifullah khan
<asifullah111@gmail.com <mailto:asifullah111@gmail.com>> wrote:

Dear Officer,

I am a new user to assemble 75bp illumina solexa data. I
have done single read illumina sequencing of my DNA of
interest. it is a single file of about 370MB. The data, in
file is initially in FASTQ format but letter the data
arrangement become in some different kind of FASTq format
inside the file. I want to convert the whole data in to
simple FASTA format using GALAXY tools. I see the
interesting videos on your site about using galaxy and it
seems very interesting.
But here i fail to upload my 370MB data file as an initial
step. I am using 100Mbp LANE networking. Are you people
preferring any other special network connection for
uploading such huge files on GALAXY.? Kindly guide in this
aspect.
Moreover Kindly if possible then send me simple perl script
and there command lines usage description for converting any
format of FASTq in to FASTA.

Regards,
Asifullah Khan
Research officer,
DNA sequencing Labs,
ICCBS, University of Karachi, Pakistan.
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